scan BAM files for total read counts

Description

scan BAM files for total read counts

Usage

totalReadCounts(x)

Arguments

Details

slow procedure – does lightweight scan of entire file

Value

named integer vector of read counts per sample

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

Examples

example(bs1)
totalReadCounts(bs1)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(leeBamViews)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: BSgenome
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/leeBamViews/totalReadCounts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: totalReadCounts
> ### Title: scan BAM files for total read counts
> ### Aliases: totalReadCounts totalReadCounts,BamViews-method
> ### Keywords: models
> 
> ### ** Examples
> 
> example(bs1)

bs1> library(leeBamViews)  # bam files stored in package

bs1> bpaths = dir(system.file("bam", package="leeBamViews"), full=TRUE, patt="bam$")

bs1> #
bs1> # extract genotype and lane information from filenames
bs1> #
bs1> gt = gsub(".*/", "", bpaths)

bs1> gt = gsub("_.*", "", gt)

bs1> lane = gsub(".*(.)$", "\1", gt)

bs1> geno = gsub(".$", "", gt)

bs1> #
bs1> # format the sample-level information appropriately
bs1> #
bs1> pd = DataFrame(geno=geno, lane=lane, row.names=paste(geno,lane,sep="."))

bs1> prd = new("DataFrame")  # protocol data could go here

bs1> #
bs1> # create the views object, adding some arbitrary experiment-level information
bs1> #
bs1> bs1 = BamViews(bamPaths=bpaths, bamSamples=pd,
bs1+         bamExperiment=list(annotation="org.Sc.sgd.db"))

bs1> bs1
BamViews dim: 0 ranges x 8 samples 
names: isowt.5 isowt.6 ... xrn.1 xrn.2 
detail: use bamPaths(), bamSamples(), bamRanges(), ... 

bs1> # add ranges and tabulate reads
bs1> 
bs1> START=c(861250, 863000)

bs1> END=c(862750, 864000)

bs1> exc = GRanges(IRanges(start=START, end=END), seqnames="Scchr13", strand="+")

bs1> values(exc)$name = c("intv1", "intv2")  # necessary

bs1> bamRanges(bs1) = exc

bs1> bs1
BamViews dim: 2 ranges x 8 samples 
names: isowt.5 isowt.6 ... xrn.1 xrn.2 
detail: use bamPaths(), bamSamples(), bamRanges(), ... 

bs1> tabulateReads(bs1, "+")
         intv1  intv2
start   861250 863000
end     862750 864000
isowt.5   3673   2697
isowt.6   3770   2653
rlp.5     1532   1047
rlp.6     1567   1140
ssr.1     4304   3065
ssr.2     4627   3388
xrn.1     2841   1695
xrn.2     3477   2199
> totalReadCounts(bs1)
isowt5_13e.bam isowt6_13e.bam   rlp5_13e.bam   rlp6_13e.bam   ssr1_13e.bam 
         34549          34552          24634          25102          32657 
  ssr2_13e.bam   xrn1_13e.bam   xrn2_13e.bam 
         35268          23513          29410 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>